BAM header file error

[Muthukumar]

I ran the following the command to extract bam file for specific chromosomal locus.

samtools view -h accepted_hits.bam "EQ963475:334376-335722">AFLA_105440.bam

The result of command was generated with header file
######first few lines output file######
@HD VN:1.0 SO:coordinate
@SQ SN:EQ963472 LN:4469204
@SQ SN:EQ963473 LN:4149026
@SQ SN:EQ963474 LN:2713190
@SQ SN:EQ963475 LN:2658400
@SQ SN:EQ963476 LN:2555871
@SQ SN:EQ963477 LN:2388123
@SQ SN:EQ963478 LN:2337902

When I ran the below command for conversion of bam to fastq

samtools bam2fq AFLA_105440.bam >AFLA_105440.fq

it showing error like this:
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).

My ultimate objective is to get fasta file from bam. Thats y I am converting bam file into fastq..... So any one please what is /are tools available for this converion

[Michael.Ante]

Hi Muthukumar,

with your first command, you generated a SAM file. In order to use samtools bam2fq, you need a bam file:

samtools view -h[B]b[/B] accepted_hits.bam "EQ963475:334376-335722">AFLA_105440.bam

That should do the job.

Cheers,
Michael

[Muthukumar]

Thank you very much its working now.

Hi Muthukumar,

with your first command, you generated a SAM file. In order to use samtools bam2fq, you need a bam file:

samtools view -h[B]b[/B] accepted_hits.bam "EQ963475:334376-335722">AFLA_105440.bam

That should do the job.

Cheers,
Michael